Analysis of non-protein coding DNA transcription for roles in regulating gene expression

During transcription, the DNA sequence encoding a gene is “read” and copied into an RNA molecule. Many RNA molecules convey instructions for synthesizing proteins. Traditionally, proteins are thought of as molecular workhorses, which perform cellular functions. However, recent work has discovered that transcription of non-protein coding DNA is widespread in eukaryotes and plays important regulatory roles for many genes including genes mis-regulated in cancers. For example, in S. cerevisiae, the act of transcribing SRG1, a non-coding RNA (ncRNA), across the SER3 promoter positions nucleosomes over the SER3 upstream activating sequences. This creates a physical barrier preventing transcription of SER3. The pervasiveness of non-coding transcription suggests that regulatory roles for non-coding transcription may exist throughout the genome. To explore this possibility, we selected six candidate yeast genes expressing ncRNAs over their promoters and analyzed the effects of disrupting intergenic transcription on neighboring protein-coding transcript expression. Through this unbiased approach, we identified a previously unknown mechanism of transcription regulation at the ECM3 gene. Intergenic transcription seems to activate ECM3 expression. Further analyses identified roles for the Paf1 complex in ECM3 activation through methylation of histone H3 at lysine 4. Additionally, the NuA3 and SAGA chromatin modifying complexes are also required to activate ECM3 expression. These data support a model where co-transcriptional methylation of histone H3 at lysine 4 is required to recruit the NuA3 complex and other downstream modifiers to activate transcription of ECM3. Other cases of regulation by intergenic transcription had previously identified this modification in negative regulation of neighboring gene expression. Thus, ECM3 is an interesting model gene for elucidation of a novel regulatory mechanism mediated by non-coding transcription. The results presented here add to the growing number of cases where noncoding transcription has important roles in regulating gene expression. This work also indicates that the molecular mechanisms by which transcription of noncoding DNA exerts regulatory effects depend on the local chromatin environment